Automated macrophage counting in DLBCL tissue samples: a ROF filter based approach

BackgroundFor analysis of the tumor microenvironment in diffuse large B-cell lymphoma (DLBCL) tissue samples, it is desirable to obtain information about counts and distribution of different macrophage subtypes. Until now, macrophage counts are mostly inferred from gene expression analysis of whole tissue sections, providing only indirect information. Direct analysis of immunohistochemically (IHC) fluorescence stained tissue samples is confronted with several difficulties, e.g. high variability of shape and size of target macrophages and strongly inhomogeneous intensity of staining. Consequently, application of commercial software is largely restricted to very rough analysis modes, and most macrophage counts are still obtained by manual counting in microarrays or high power fields, thus failing to represent the heterogeneity of tumor microenvironment adequately.MethodsWe describe a Rudin-Osher-Fatemi (ROF) filter based segmentation approach for whole tissue samples, combining floating intensity thresholding and rule-based feature detection. Method is validated against manual counts and compared with two commercial software kits (Tissue Studio 64, Definiens AG, and Halo, Indica Labs) and a straightforward machine-learning approach in a set of 50 test images. Further, the novel method and both commercial packages are applied to a set of 44 whole tissue sections. Outputs are compared with gene expression data available for the same tissue samples. Finally, the ROF based method is applied to 44 expert-specified tumor subregions for testing selection and subsampling strategies.ResultsAmong all tested methods, the novel approach is best correlated with manual count (0.9297). Automated detection of evaluation subregions proved to be fully reliable. Comparison with gene expression data obtained for the same tissue samples reveals only moderate to low correlation levels. Subsampling within tumor subregions is possible with results almost identical to full sampling. Mean macrophage size in tumor subregions is 152.5111.3 ...